This project This web page originated as an assignment in Emory University's Biology 142 lab course. Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein. This specific wiki page assesses ERAP1.
Background Information ERAP1 is active in the endoplasmic reticulum [5]. The full name for ERAP1 is endoplasmic reticulum aminopeptidase 1 [5]. The protein is 948 amino acids in length and belongs to the domain peptidase M1 which is part of the clan MA [5,7]. The protein structure can be seen in figure 2. The protein has two major functions including the ability to cleave several cytokine receptors on the surface of cells, which reduces their ability to transmit chemical signals to the cells and affects the process of inflammation and the ability to cleave proteins into small peptides that can be recognized by the immune system, as seen in figure 1 [5]. ERAP1 has been linked to inflammation disorders including Ankylosing spondylitis, Psoriasis, Crohn's disease, and more [2,3,10,11].
Figure 1. (left) Peptide fragments are transported to the ER where they are further trimmed to 8 or 9 amino acids by ERAP1 [6]. Figure 2. (right) Shape of ERAP1 represented as a ribbon diagram, color coded by domain with dotted lines representing disordered loops [6].
Methods The FASTA sequence for ERAP1 was obtained using its ID (ENSP00000296754) through Ensembl [4]. Then, The Georgia Aquarium Galaxy Server [8] was utilized to run a protein BLAST of the human protein sequence for ERAP1 as the query against the predicted whale shark protein database. The FASTA sequence was extracted for the top five chosen proteins. Each FASTA sequence was then blasted against the NCBI human protein database [1] to find the best match. The human sequence was the blasted against the mouse, zebra fish, yeast, clawed frog, dog, and elephant shark using the NCBI again to assess similarities across species. The FASTA sequences were extracted and Clustlaw [9] was used to form a phylogenic tree.
Whale Shark Protein Research The top five results as shown in figure 3 for the whale shark genome were chosen based on e-value or percent value to be blasted against the human genome to see which is most closely related to the ERAP1 protein in humans. While traditionally, query coverage is also used as a predictor, the whale shark gene with the second smallest alignment length actually ended up being the best match. Figure 3. The FASTA sequence for ERAP1 was blasted against the whale shark genome through the Georgia Aquarium and results were returned for similar protein sequences. The highlighted sequences include two with the highest e-vale and three with the highest percent identity to approach the protein sequence from two ways.
Protein Domain The most likely ortholog in the whale shark protein database is endoplasmic reticulum aminopeptidase 1 isoform b precursor which belongs to the domain peptidase M1. The rest of the species also express endoplasmic reticulum aminopeptidases, except yeast. The peptidase M1 family contains mainly aminopeptidases that are activated by the zinc ion. The family is based on aminopeptidase N, found in humans.
Comparing Species: Orthologs The human protein sequence for ERAP1, when blasted against the whale shark, mouse, zebra fish, yeast, clawed frog, dog, and elephant, found endoplasmic reticulum aminopeptidase in each species except in yeast. However, different forms of the protein were found in each species, linking some species more closely than others as shown in figure 5. For example, the elephant shark is related marginally because it has endoplasmic reticulum aminopeptidase 2 while humans have endoplasmic reticulum amino peptidase 1. The whale shark shows to have an ortholog of endoplasmic reticulum amino peptidase 1 but as noted in figure 4, it is a precursor and is predicted by the Georgia Aquarium.
Figure 4. This table is a compilation of the protein sequence information for the top five matching whale shark sequences as well as the most closely related protein sequences from a mouse, zebra fish, yeast, clawed frog, dog, and elephant shark when blasted against the human protein sequence for ERAP1.
Figure 5. The phylogenic tree compares the most closely related protein to ERAP1 in each species to ERAP1 in humans [9].
Conclusion: After careful analysis of the mouse, dog, clawed frog, zebra fish, elephant shark, whale shark, and yeast for the ERAP1 protein, it is clear that the inflammatory protein is present in each species except yeast. However, there are variations of the protein and it is only predicted thus far in the whale shark. This suggests that the whale shark may have some similarities in inflammatory response to humans and other species. One question the results raised was why, if the human and whale shark express ERAP1, is the elephant shark more closely related to the human when it expresses ERAP2? As seen in Figure 4, yeast is the only organism studied that does not express any endoplasmic reticulum aminopeptidase. This raises the question for future studies of whether or not endoplasmic reticulum aminopeptidase is something expressed solely in all multicellular eukaryotes.
ERAP1: endoplasmic reticulum aminopeptidase 1
Sabrina Madni, Kavita Athalye, Ashley GrahamThis project
This web page originated as an assignment in Emory University's Biology 142 lab course.
Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein. This specific wiki page assesses ERAP1.
Background Information
ERAP1 is active in the endoplasmic reticulum [5]. The full name for ERAP1 is endoplasmic reticulum aminopeptidase 1 [5]. The protein is 948 amino acids in length and belongs to the domain peptidase M1 which is part of the clan MA [5,7]. The protein structure can be seen in figure 2. The protein has two major functions including the ability to cleave several cytokine receptors on the surface of cells, which reduces their ability to transmit chemical signals to the cells and affects the process of inflammation and the ability to cleave proteins into small peptides that can be recognized by the immune system, as seen in figure 1 [5]. ERAP1 has been linked to inflammation disorders including Ankylosing spondylitis, Psoriasis, Crohn's disease, and more [2,3,10,11].
Figure 1. (left) Peptide fragments are transported to the ER where they are further trimmed to 8 or 9 amino acids by ERAP1 [6].
Figure 2. (right) Shape of ERAP1 represented as a ribbon diagram, color coded by domain with dotted lines representing disordered loops [6].
Methods
The FASTA sequence for ERAP1 was obtained using its ID (ENSP00000296754) through Ensembl [4]. Then, The Georgia Aquarium Galaxy Server [8] was utilized to run a protein BLAST of the human protein sequence for ERAP1 as the query against the predicted whale shark protein database. The FASTA sequence was extracted for the top five chosen proteins. Each FASTA sequence was then blasted against the NCBI human protein database [1] to find the best match. The human sequence was the blasted against the mouse, zebra fish, yeast, clawed frog, dog, and elephant shark using the NCBI again to assess similarities across species. The FASTA sequences were extracted and Clustlaw [9] was used to form a phylogenic tree.
Whale Shark Protein Research
The top five results as shown in figure 3 for the whale shark genome were chosen based on e-value or percent value to be blasted against the human genome to see which is most closely related to the ERAP1 protein in humans. While traditionally, query coverage is also used as a predictor, the whale shark gene with the second smallest alignment length actually ended up being the best match.
Figure 3. The FASTA sequence for ERAP1 was blasted against the whale shark genome through the Georgia Aquarium and results were returned for similar protein sequences. The highlighted sequences include two with the highest e-vale and three with the highest percent identity to approach the protein sequence from two ways.
Protein Domain
The most likely ortholog in the whale shark protein database is endoplasmic reticulum aminopeptidase 1 isoform b precursor which belongs to the domain peptidase M1. The rest of the species also express endoplasmic reticulum aminopeptidases, except yeast. The peptidase M1 family contains mainly aminopeptidases that are activated by the zinc ion. The family is based on aminopeptidase N, found in humans.
Comparing Species: Orthologs
The human protein sequence for ERAP1, when blasted against the whale shark, mouse, zebra fish, yeast, clawed frog, dog, and elephant, found endoplasmic reticulum aminopeptidase in each species except in yeast. However, different forms of the protein were found in each species, linking some species more closely than others as shown in figure 5. For example, the elephant shark is related marginally because it has endoplasmic reticulum aminopeptidase 2 while humans have endoplasmic reticulum amino peptidase 1. The whale shark shows to have an ortholog of endoplasmic reticulum amino peptidase 1 but as noted in figure 4, it is a precursor and is predicted by the Georgia Aquarium.
Figure 4. This table is a compilation of the protein sequence information for the top five matching whale shark sequences as well as the most closely related protein sequences from a mouse, zebra fish, yeast, clawed frog, dog, and elephant shark when blasted against the human protein sequence for ERAP1.
Figure 5. The phylogenic tree compares the most closely related protein to ERAP1 in each species to ERAP1 in humans [9].
Conclusion:
After careful analysis of the mouse, dog, clawed frog, zebra fish, elephant shark, whale shark, and yeast for the ERAP1 protein, it is clear that the inflammatory protein is present in each species except yeast. However, there are variations of the protein and it is only predicted thus far in the whale shark. This suggests that the whale shark may have some similarities in inflammatory response to humans and other species. One question the results raised was why, if the human and whale shark express ERAP1, is the elephant shark more closely related to the human when it expresses ERAP2? As seen in Figure 4, yeast is the only organism studied that does not express any endoplasmic reticulum aminopeptidase. This raises the question for future studies of whether or not endoplasmic reticulum aminopeptidase is something expressed solely in all multicellular eukaryotes.
References: